ORIGINAL PAPER Development of COS-SNP and HRM markers for high- throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.) Irma Terracciano • Marco Maccaferri • Filippo Bassi • Paola Mantovani • Maria C. Sanguineti • Silvio Salvi • Hana S ˇ imkova ´ • Jaroslav Dolez ˇel • Andrea Massi • Karim Ammar • James Kolmer • Roberto Tuberosa Received: 21 September 2012 / Accepted: 17 December 2012 / Published online: 5 January 2013 Ó Springer-Verlag Berlin Heidelberg 2013 Abstract Leaf rust (Puccinia triticina Eriks. & Henn.) is a major disease affecting durum wheat production. The Lr14a-resistant gene present in the durum wheat cv. Creso and its derivative cv. Colosseo is one of the best charac- terized leaf-rust resistance sources deployed in durum wheat breeding. Lr14a has been mapped close to the simple sequence repeat markers gwm146, gwm344 and wmc10 in the distal portion of the chromosome arm 7BL, a gene- dense region. The objectives of this study were: (1) to enrich the Lr14a region with single nucleotide polymor- phisms (SNPs) and high-resolution melting (HRM)-based markers developed from conserved ortholog set (COS) genes and from sequenced Diversity Array Technology (DArT Ò ) markers; (2) to further investigate the gene con- tent and colinearity of this region with the Brachypodium and rice genomes. Ten new COS-SNP and five HRM markers were mapped within an 8.0 cM interval spanning Lr14a. Two HRM markers pinpointed the locus in an interval of \ 1.0 cM and eight COS-SNPs were mapped 2.1–4.1 cM distal to Lr14a. Each marker was tested for its capacity to predict the state of Lr14a alleles (in particular, Lr14-Creso associated to resistance) in a panel of durum wheat elite germplasm including 164 accessions. Two of the most informative markers were converted into KAS- Par Ò markers. Single assay markers ubw14 and wPt-4038- HRM designed for agarose gel electrophoresis/KASPar Ò assays and high-resolution melting analysis, respectively, as well as the double-marker combinations ubw14/ubw18, ubw14/ubw35 and wPt-4038-HRM–ubw35 will be useful for germplasm haplotyping and for molecular-assisted breeding. Introduction Durum wheat (Triticum turgidum ssp. durum Desf.) is an important cereal crop adapted, among others, to the Med- iterranean region where it is the main cultivated cereal and produces staple foods for tens of millions of people. It is also grown in the Northern Prairies of USA and Canada, Southwestern USA, Mexico, Central Asian regions, Central India and Australia. Throughout these regions, crop Communicated by P. Langridge. Electronic supplementary material The online version of this article (doi:10.1007/s00122-012-2038-9) contains supplementary material, which is available to authorized users. I. Terracciano Á M. Maccaferri (&) Á F. Bassi Á P. Mantovani Á M. C. Sanguineti Á S. Salvi Á R. Tuberosa Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, Bologna 40127, Italy e-mail: marco.maccaferri@unibo.it F. Bassi Department of Plant Sciences, North Dakota State University, 166 N. Bolley Dr, Fargo, ND 58102, USA P. Mantovani Á A. Massi Societa ` Produttori Sementi Bologna, Via Macero 1, Argelato, Bologna 40050, Italy H. S ˇ imkova ´ Á J. Dolez ˇel Institute of Experimental Botany, Sokolovska 6, 77200 Olomouc, Czech Republic K. Ammar CIMMYT, Carretera Mexico-Veracruz KM. 45, 56130 Texcoco, Mexico J. Kolmer Cereal Disease Laboratory, Agricultural Research Service, US Department of Agriculture, 1551 Lindig Avenue, St. Paul, MN 55108, USA 123 Theor Appl Genet (2013) 126:1077–1101 DOI 10.1007/s00122-012-2038-9